rs3019279

Variant names:

• chr8-94435677-G-C
• rs3019279
• NM_012415.3:c.304+22591C>G

Your query was ambiguous. Multiple possible variants found:

• chr8-94435677-G-C
• chr8-94435677-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012415.3(RAD54B):​c.304+22591C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,766 control chromosomes in the GnomAD database, including 12,730 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (12730 hom., cov: 32)
• Consequence: RAD54B NM_012415.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 2 publications found

Genes affected

RAD54B (HGNC:17228): (RAD54 homolog B) The protein encoded by this gene belongs to the DEAD-like helicase superfamily. It shares similarity with Saccharomyces cerevisiae RAD54 and RDH54, both of which are involved in homologous recombination and repair of DNA. This protein binds to double-stranded DNA, and displays ATPase activity in the presence of DNA. This gene is highly expressed in testis and spleen, which suggests active roles in meiotic and mitotic recombination. Homozygous mutations of this gene were observed in primary lymphoma and colon cancer. [provided by RefSeq, Jul 2008]

FSBP (HGNC:43653): (fibrinogen silencer binding protein) Enables identical protein binding activity. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAD54B	NM_012415.3	c.304+22591C>G		intron_variant	Intron 3 of 14	ENST00000336148.10	NP_036547.1
FSBP	NM_001256141.2	c.374+818C>G		intron_variant	Intron 1 of 1	ENST00000481490.3	NP_001243070.1
RAD54B	NM_001205263.2	c.-249+818C>G		intron_variant	Intron 1 of 12		NP_001192192.1
RAD54B	NM_001205262.3	c.305-3021C>G		intron_variant	Intron 3 of 3		NP_001192191.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAD54B	ENST00000336148.10	c.304+22591C>G		intron_variant	Intron 3 of 14	1	NM_012415.3	ENSP00000336606.5
FSBP	ENST00000481490.3	c.374+818C>G		intron_variant	Intron 1 of 1	1	NM_001256141.2	ENSP00000420405.2

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61780 AN: 151648 Hom.: 12725 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.429

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.407 AC: 61821 AN: 151766 Hom.: 12730 Cov.: 32 AF XY: 0.414 AC XY: 30683 AN XY: 74150

African (AFR) AF: 0.407 AC: 16846 AN: 41388

American (AMR) AF: 0.505 AC: 7705 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1300 AN: 3462

East Asian (EAS) AF: 0.465 AC: 2397 AN: 5150

South Asian (SAS) AF: 0.425 AC: 2047 AN: 4816

European-Finnish (FIN) AF: 0.434 AC: 4571 AN: 10534

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.378 AC: 25643 AN: 67862

Other (OTH) AF: 0.425 AC: 897 AN: 2110

Alfa AF: 0.403 Hom.: 1723

Bravo AF: 0.414

Asia WGS AF: 0.426 AC: 1478 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.64
PhyloP100		-0.25
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3019279; hg19: chr8-95447905;